A comparative genomics approach to identifying the plasticity transcriptome

Pfenning, Andreas R; Schwartz, Russell; Barth, Alison L

doi:10.1186/1471-2202-8-20

Table 3 Overlapping regulatory targets: comparison with other studies

From: A comparative genomics approach to identifying the plasticity transcriptome

Symbol	Gene Name	Accession #^a	Conserved site^b	Type of study^c	Reference
Clcn3	chloride channel 3	NM007711	CREB	ChIP/SACO	25
Cycs	cytochrome c, somatic	NM007808	CREB	ChIP/SACO	25
Fn1	fibronectin 1	AK147683	CREB	ChIP/SACO	25
FosB	FosB	NM008036	CREB	ChIP/SACO	25
Ldh1	lactate dehydrogenase 1, A chain	BC066858	CREB	ChIP/SACO	25
Mlf2	myeloid leukemia factor 2	NM145385	CREB	ChIP/SACO	25
Nf1	neurofibromatosis 1	NM010897	CREB	ChIP/SACO	25
Ppargc2	peroxisome proliferative activated receptor, gamma, coactivator 1 alpha	NM008904	CREB	ChIP/SACO	25
Sstr2	somatostatin receptor 2	NM009217	CREB	ChIP/SACO	25
St13	suppression of tumorigenicity 13	NM133726	CREB	ChIP/SACO	25
Socs7	suppressor of cytokine signaling 7	NM138657	CREB	ChIP/SACO	25
TpT1	tumor protein, translationally-controlled 1	NM009429	CREB	ChIP/SACO	25
JunD1	Jun proto-oncogene related gene d1	NM010592, 16478	CREB	ChIP/SACO, CREB overexpression	25, 37
Maff	v-maf musculoaponeurotic fibrosarcoma oncogene family, protein F (avian)	NM_010755, 17133	CREB	ChIP/SACO, CREB overexpression	25, 37
Arg2	arginase type II	11847	CREB	CREB overexpression	37
Avpi1	arginine vasopressin-induced 1	69534	CREB	CREB overexpression	37
Arih1	ariadne ubiquitin-conjugating enzyme E2 binding protein homolog 1 (Drosophila)	23806	CREB	CREB overexpression	37
Cd2ap	CD2-associated protein	12488	CREB	CREB overexpression	37
Dhx36	DEAH (Asp-Glu-Ala-His) box polypeptide 36	72162	CREB	CREB overexpression	37
Dusp1	dual specificity phosphatase 1	19252	CREB	CREB overexpression	37
Ell2	elongation factor RNA polymerase II 2	192657	CREB	CREB overexpression	37
AW050020	expressed sequence AW050020	268420	CREB	CREB overexpression	37
Foxd3	forkhead box D3	15221	CREB	CREB overexpression	37
Gem	GTP binding protein (gene overexpressed in skeletal muscle)	14579	CREB	CREB overexpression	37
Mcm2	minichromosome maintenance deficient 2 mitotin (S. cerevisiae)	17216	CREB	CREB overexpression	37
Mlf1	myeloid leukemia factor 1	17349	CREB	CREB overexpression	37
Myh10	myosin, heavy polypeptide 10, non-muscle	77579	CREB	CREB overexpression	37
Nek1	NIMA (never in mitosis gene a)-related expressed kinase 1	18004	CREB	CREB overexpression	37
Pde7a	phosphodiesterase 7A	18583	CREB	CREB overexpression	37
Psmb8	proteosome (prosome, macropain) subunit, beta type 8 (large multifunctional peptidase 7)	16913	CREB	CREB overexpression	37
2700085E05Rik	RIKEN cDNA 2700085E05 gene	67201	CREB	CREB overexpression	37
4933407C03Rik	RIKEN cDNA 4933407C03 gene	74440	CREB	CREB overexpression	37
6330407G11Rik	RIKEN cDNA 6330407G11 gene	68050	CREB	CREB overexpression	37
Rbms2	RNA binding motif, single stranded interacting protein 2	56516	CREB	CREB overexpression	37
St7	Suppression of tumorigenicity 7	64213	CREB	CREB overexpression	37
Tgif2	TGFB-induced factor 2	228839	CREB	CREB overexpression	37
Trip6	thyroid hormone receptor interactor 6	22051	CREB	CREB overexpression	37
Tle3	transducin-like enhancer of split 3, homolog of Drosophila E(spl)	21887	CREB	CREB overexpression	37
Tpm4	tropomyosin 4	326618	CREB	CREB overexpression	37
Trp53inp2	tumor protein p53 inducible nuclear protein 2	68728	CREB	CREB overexpression	37
Th	tyrosine hydroxylase	21823	CREB	CREB overexpression	37
Wbp5	WW domain binding protein 5	22381	CREB	CREB overexpression	37
Xpr1	xenotropic and polytropic retrovirus receptor 1	19775	CREB	CREB overexpression	37
Znrd1	zinc ribbon domain containing, 1	66136	CREB	CREB overexpression	37
Sgta	small glutamine-rich tetratricopeptide repeat (TPR)-containing, alpha	NM024499	Zif268	Zif268 overexpression	57

^aAccession numbers for CREB overexpression experiments are the GeneID, not the mRNA acession number.
^bGene target had a conserved mouse-human transcription factor binding site in the promoter region and was also identified in the referenced study.
^cType of experimental analysis carried out in the referenced study. ChIP indicated chromatin immunoprecipitation followed by a serial analysis of chromatin occupancy in DNA isolated from rat PC12 cells that had been stimulated with forskolin to increase intracellular cAMP 15 minutes prior to DNA extraction [25]. Zif268 overexpression refers to studies where zif268 was overexpressed in PC12 cells, and RNA was extracted 48 hrs post-transfection [57]. CREB overexpression refers to studies where a super-active form of CREB is expressed in mice for 1 to 5 weeks. RNA is extracted from hippocampus and run on Affymetrix GeneChip Murine Genome U74 Version 2 Set MG-U74A [37]. Our analysis of the data was done using GSEA as described in the methods.

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